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No - you cannot control the name that way either. It is likely that at some point in the future you will be able to do so as user defined file masks are on the development plans. However there is no timescale as to when that might happen.
There is definitely no limit like you mention in terms of file size for epub - the vast majority of mine are larger than that.
In terms of the best format to keep ebooks in, PDF is probably the worst format as it is extremely difficult to convert to other formats reliably.
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